Hi Thibault, It seems to me that what your copy_torsion() function really wants is just two residues. I'd have your command register just a ResiduesArg (from chimerax.atomic) and have your function take just 'session' and 'residues' args. The function could check if len(residues) == 2 if you wanted. You would copy the psi angle from the second residue to the first with residues[0].psi = residues[1].psi. Phi/omega would work the same way. What you would then type to your command would be something like "copyTorsion #1:231 #2:231". --Eric Eric Pettersen UCSF Computer Graphics Lab

On Oct 31, 2022, at 6:52 AM, Thibault TUBIANA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi!

I would like to create a function to copy the torsion angle from a model to another one. The function would take in argument the model ID of the reference and target model (<int>) and the residue id (<int>). I looked a bit at the scripts available in https://rbvi.github.io/chimerax-recipes/ <https://rbvi.github.io/chimerax-recipes/> to have an idea of how to add function in ChimeraX, but I'm currently stuck at "how to get the list of atoms from a selection string ?".

Here's my current script from chimerax.core.commands import run

def copy_torsion(session, model1, model2, residue): selection = f"torsion #{model2}:{residue}@n,ca,c:{residue+1}@n" from chimerax.atomic import AtomsArg

atoms = AtomsArg(selection)

from chimerax.geometry import dihedral cur_torsion = dihedral([*a.scene_coord for a in atoms])

torsion=run(session, f"torsion #{model1}:{residue}@n,ca,c:{residue+1}@n {cur_torsion}")

def register_command(logger): from chimerax.core.commands import CmdDesc, register, FloatArg, IntArg, BoolArg, Color8Arg, StringArg from chimerax.atomic import AtomsArg desc = CmdDesc(required = [ ('model1', IntArg), ('model2', IntArg), ('residue', IntArg), ], synopsis='Copy torsion angle') register('copyTorsion', desc, copy_torsion, logger=logger)

register_command(session) Thank you for your help :)

Best regards, Thibault.

-- Thibault Tubiana, PhD Postdoctoral Fellow @IMAPP <https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanisms...> Institute for integrative biology of the cell (I2BC <https://www.i2bc.paris-saclay.fr/>) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: http://www.tubiana.me/ <http://www.tubiana.me/>

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Hi Tom! Thank you so much for your help, especially with the command allowing a residue range that's perfect =D Best regards, Thibault. De: "Tom Goddard" <goddard@sonic.net> À: "Thibault TUBIANA" <thibault.tubiana@i2bc.paris-saclay.fr> Cc: "chimerax-users" <ChimeraX-users@cgl.ucsf.edu> Envoyé: Lundi 31 Octobre 2022 18:29:27 Objet: Re: [chimerax-users] Get atom from selection string in script Hi Thibault, I suggest you make your command syntax like this copyTorsion #1:78 to #2 This will be a more familiar way of specifying command arguments in ChimeraX. Also it is easy to get the torsion angle and set it using the residue "psi" angle. Here is a modified version of your code. It allows specifying multiple residues also ("copytor #1:55-65 to #2"). Tom def copy_torsion(session, residues, to_structure): for residue in residues: res_num = residue.number cmd = f"torsion {to_structure.atomspec}:{res_num}@n,ca,c:{res_num+1}@n {residue.psi}" from chimerax.core.commands import run run(session, cmd) def register_command(logger): from chimerax.core.commands import CmdDesc, register from chimerax.atomic import ResiduesArg, AtomicStructureArg desc = CmdDesc(required = [ ('residues', ResiduesArg) ], keyword = [ ('to_structure', AtomicStructureArg) ], required_arguments = ['to_structure'], synopsis='Copy torsion angle') register('copytorsion', desc, copy_torsion, logger=logger) register_command(session.logger) On Oct 31, 2022, at 6:52 AM, Thibault TUBIANA via ChimeraX-users < [ mailto:chimerax-users@cgl.ucsf.edu | chimerax-users@cgl.ucsf.edu ] > wrote: Hi! I would like to create a function to copy the torsion angle from a model to another one. The function would take in argument the model ID of the reference and target model (<int>) and the residue id (<int>). I looked a bit at the scripts available in [ https://rbvi.github.io/chimerax-recipes/ | https://rbvi.github.io/chimerax-recipes/ ] to have an idea of how to add function in ChimeraX, but I'm currently stuck at "how to get the list of atoms from a selection string ?". Here's my current script from chimerax.core.commands import run def copy_torsion(session, model1, model2, residue): selection = f"torsion #{model2}:{residue}@n,ca,c:{residue+1}@n" from chimerax.atomic import AtomsArg atoms = AtomsArg(selection) from chimerax.geometry import dihedral cur_torsion = dihedral([*a.scene_coord for a in atoms]) torsion=run(session, f"torsion #{model1}:{residue}@n,ca,c:{residue+1}@n {cur_torsion}") def register_command(logger): from chimerax.core.commands import CmdDesc, register, FloatArg, IntArg, BoolArg, Color8Arg, StringArg from chimerax.atomic import AtomsArg desc = CmdDesc(required = [ ('model1', IntArg), ('model2', IntArg), ('residue', IntArg), ], synopsis='Copy torsion angle') register('copyTorsion', desc, copy_torsion, logger=logger) register_command(session) Thank you for your help :) Best regards, Thibault. -- Thibault Tubiana, PhD Postdoctoral Fellow @ [ https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanisms... | IMAPP ] Institute for integrative biology of the cell ( [ https://www.i2bc.paris-saclay.fr/ | I2BC ] ) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: [ http://www.tubiana.me/ | http://www.tubiana.me/ ] _______________________________________________ ChimeraX-users mailing list [ mailto:ChimeraX-users@cgl.ucsf.edu | ChimeraX-users@cgl.ucsf.edu ] Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users